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The wheat tribe, Triticeae, includes many genomically distinct polyploid taxa. Elymus is an entirely allopolyploid genus, with all species containing the St genome of Pseudoroegneria. The St genome may be combined with one or more distinct genomes representing multiple, diverse diploid donors from throughout the tribe. This study includes a simultaneous phylogenetic analysis of new and previously published data from several distinct Elymus groups, including North American and Eurasian StStHH tetraploids, in which the H genome is derived from Hordeum, Eurasian StStYY tetraploids, in which the Y genome is derived from an unknown donor, and a putative StStStStHH hexaploid. Elymus species were analyzed with a broad sample of diploid genera from within the tribe using a combination of molecular data from the chloroplast and the nuclear genomes. The data confirm the genomic constitution of the StStHH and StStYY tetraploids, but do not provide additional information on the identity of the Y-genome donor. The genomic diversity in the hexaploid is greater than expected, inconsistent with the hypothesis of an StStStStHH genome complement.